Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943
A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogo...
Gespeichert in:
| Veröffentlicht in: | DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes 2008-10, Vol.15 (5), p.285-295 |
|---|---|
| Hauptverfasser: | , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext bestellen |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 295 |
|---|---|
| container_issue | 5 |
| container_start_page | 285 |
| container_title | DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes |
| container_volume | 15 |
| creator | Lu, Tingting Yu, Shuliang Fan, Danlin Mu, Jie Shangguan, Yingying Wang, Zixuan Minobe, Yuzo Lin, Zhixin Han, Bin |
| description | A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, |
| doi_str_mv | 10.1093/dnares/dsn018 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_TOX</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2575888</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/dnares/dsn018</oup_id><sourcerecordid>20250828</sourcerecordid><originalsourceid>FETCH-LOGICAL-c545t-f45964b42c3849f6ef4a55b3110fac2db4c5952591bf30a88adeb2b76dab82aa3</originalsourceid><addsrcrecordid>eNqFkc9rFTEQxxdR7A89epVclF62ze9NLsLjaatQLIjSY5jNJq-R7GZNdgvPv94t-6h66mkG5sNnZvhW1RuCzwnW7KIbILty0ZUBE_WsOiaNkDWRkj1fesZxTRVTR9VJKT8x5kSw5mV1RJRUjWz4cRW2KUZnp5AGBEOHtqkfIcMU7h3aDBD3JRSUPCJKKXQ5x1hHN-ymO2Q_ft0U5HPq0W2IHfoWrEM3ef8bUJ59GNNuMV7l4P05uiWas1fVCw-xuNeHelr9uPz0ffu5vr65-rLdXNdWcDHVngstecupZYprL53nIETLCMEeLO1aboUWVGjSeoZBKehcS9tGdtAqCsBOqw-rd5zb3nXWDVOGaMYcesh7kyCY_ydDuDO7dG-oaMTy5SJ4fxDk9Gt2ZTJ9KNbFCINLczFSS90wLZ4EKaYCK_pgrFfQ5lRKdv7xGoLNQ4pmTdGsKS78239f-EsfYluAdwcAioXoMww2lEeO4kYrzvXCna1cmscndv4Bhgm1lA</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>20250828</pqid></control><display><type>article</type><title>Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943</title><source>Access via Oxford University Press (Open Access Collection)</source><creator>Lu, Tingting ; Yu, Shuliang ; Fan, Danlin ; Mu, Jie ; Shangguan, Yingying ; Wang, Zixuan ; Minobe, Yuzo ; Lin, Zhixin ; Han, Bin</creator><contributor>Yano, M</contributor><creatorcontrib>Lu, Tingting ; Yu, Shuliang ; Fan, Danlin ; Mu, Jie ; Shangguan, Yingying ; Wang, Zixuan ; Minobe, Yuzo ; Lin, Zhixin ; Han, Bin ; Yano, M</creatorcontrib><description>A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, <22% of them were fully matched to the cv. Nipponbare genome sequence. The comparative analysis showed that O. rufipogon W1943 had greater similarity to O. sativa ssp. japonica than to ssp. indica cultivars. In addition, 17 novel rice cDNAs were identified, and 41 putative tissue-specific expression genes were defined through searching the rice massively parallel signature-sequencing database. In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies.</description><identifier>ISSN: 1340-2838</identifier><identifier>EISSN: 1756-1663</identifier><identifier>EISSN: 1875-6190</identifier><identifier>DOI: 10.1093/dnares/dsn018</identifier><identifier>PMID: 18687674</identifier><language>eng</language><publisher>Oxford: Oxford University Press</publisher><subject>Base Sequence ; Biological and medical sciences ; Chromosome Mapping ; Chromosomes, Plant ; Databases, Nucleic Acid ; DNA, Complementary - genetics ; DNA, Plant - genetics ; Fundamental and applied biological sciences. Psychology ; Genes. Genome ; Genetics of eukaryotes. Biological and molecular evolution ; Genome, Plant ; Molecular and cellular biology ; Molecular genetics ; Oryza - genetics ; Oryza rufipogon ; Oryza sativa</subject><ispartof>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 2008-10, Vol.15 (5), p.285-295</ispartof><rights>The Author 2008. Kazusa DNA Research Institute 2008</rights><rights>2008 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c545t-f45964b42c3849f6ef4a55b3110fac2db4c5952591bf30a88adeb2b76dab82aa3</citedby><cites>FETCH-LOGICAL-c545t-f45964b42c3849f6ef4a55b3110fac2db4c5952591bf30a88adeb2b76dab82aa3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575888/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575888/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/dnares/dsn018$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=20798449$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18687674$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Yano, M</contributor><creatorcontrib>Lu, Tingting</creatorcontrib><creatorcontrib>Yu, Shuliang</creatorcontrib><creatorcontrib>Fan, Danlin</creatorcontrib><creatorcontrib>Mu, Jie</creatorcontrib><creatorcontrib>Shangguan, Yingying</creatorcontrib><creatorcontrib>Wang, Zixuan</creatorcontrib><creatorcontrib>Minobe, Yuzo</creatorcontrib><creatorcontrib>Lin, Zhixin</creatorcontrib><creatorcontrib>Han, Bin</creatorcontrib><title>Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943</title><title>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</title><addtitle>DNA Res</addtitle><description>A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, <22% of them were fully matched to the cv. Nipponbare genome sequence. The comparative analysis showed that O. rufipogon W1943 had greater similarity to O. sativa ssp. japonica than to ssp. indica cultivars. In addition, 17 novel rice cDNAs were identified, and 41 putative tissue-specific expression genes were defined through searching the rice massively parallel signature-sequencing database. In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies.</description><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>Chromosome Mapping</subject><subject>Chromosomes, Plant</subject><subject>Databases, Nucleic Acid</subject><subject>DNA, Complementary - genetics</subject><subject>DNA, Plant - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes. Genome</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genome, Plant</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Oryza - genetics</subject><subject>Oryza rufipogon</subject><subject>Oryza sativa</subject><issn>1340-2838</issn><issn>1756-1663</issn><issn>1875-6190</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc9rFTEQxxdR7A89epVclF62ze9NLsLjaatQLIjSY5jNJq-R7GZNdgvPv94t-6h66mkG5sNnZvhW1RuCzwnW7KIbILty0ZUBE_WsOiaNkDWRkj1fesZxTRVTR9VJKT8x5kSw5mV1RJRUjWz4cRW2KUZnp5AGBEOHtqkfIcMU7h3aDBD3JRSUPCJKKXQ5x1hHN-ymO2Q_ft0U5HPq0W2IHfoWrEM3ef8bUJ59GNNuMV7l4P05uiWas1fVCw-xuNeHelr9uPz0ffu5vr65-rLdXNdWcDHVngstecupZYprL53nIETLCMEeLO1aboUWVGjSeoZBKehcS9tGdtAqCsBOqw-rd5zb3nXWDVOGaMYcesh7kyCY_ydDuDO7dG-oaMTy5SJ4fxDk9Gt2ZTJ9KNbFCINLczFSS90wLZ4EKaYCK_pgrFfQ5lRKdv7xGoLNQ4pmTdGsKS78239f-EsfYluAdwcAioXoMww2lEeO4kYrzvXCna1cmscndv4Bhgm1lA</recordid><startdate>20081001</startdate><enddate>20081001</enddate><creator>Lu, Tingting</creator><creator>Yu, Shuliang</creator><creator>Fan, Danlin</creator><creator>Mu, Jie</creator><creator>Shangguan, Yingying</creator><creator>Wang, Zixuan</creator><creator>Minobe, Yuzo</creator><creator>Lin, Zhixin</creator><creator>Han, Bin</creator><general>Oxford University Press</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20081001</creationdate><title>Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943</title><author>Lu, Tingting ; Yu, Shuliang ; Fan, Danlin ; Mu, Jie ; Shangguan, Yingying ; Wang, Zixuan ; Minobe, Yuzo ; Lin, Zhixin ; Han, Bin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c545t-f45964b42c3849f6ef4a55b3110fac2db4c5952591bf30a88adeb2b76dab82aa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>Chromosome Mapping</topic><topic>Chromosomes, Plant</topic><topic>Databases, Nucleic Acid</topic><topic>DNA, Complementary - genetics</topic><topic>DNA, Plant - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes. Genome</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genome, Plant</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Oryza - genetics</topic><topic>Oryza rufipogon</topic><topic>Oryza sativa</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lu, Tingting</creatorcontrib><creatorcontrib>Yu, Shuliang</creatorcontrib><creatorcontrib>Fan, Danlin</creatorcontrib><creatorcontrib>Mu, Jie</creatorcontrib><creatorcontrib>Shangguan, Yingying</creatorcontrib><creatorcontrib>Wang, Zixuan</creatorcontrib><creatorcontrib>Minobe, Yuzo</creatorcontrib><creatorcontrib>Lin, Zhixin</creatorcontrib><creatorcontrib>Han, Bin</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Lu, Tingting</au><au>Yu, Shuliang</au><au>Fan, Danlin</au><au>Mu, Jie</au><au>Shangguan, Yingying</au><au>Wang, Zixuan</au><au>Minobe, Yuzo</au><au>Lin, Zhixin</au><au>Han, Bin</au><au>Yano, M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943</atitle><jtitle>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</jtitle><addtitle>DNA Res</addtitle><date>2008-10-01</date><risdate>2008</risdate><volume>15</volume><issue>5</issue><spage>285</spage><epage>295</epage><pages>285-295</pages><issn>1340-2838</issn><eissn>1756-1663</eissn><eissn>1875-6190</eissn><abstract>A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, <22% of them were fully matched to the cv. Nipponbare genome sequence. The comparative analysis showed that O. rufipogon W1943 had greater similarity to O. sativa ssp. japonica than to ssp. indica cultivars. In addition, 17 novel rice cDNAs were identified, and 41 putative tissue-specific expression genes were defined through searching the rice massively parallel signature-sequencing database. In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies.</abstract><cop>Oxford</cop><pub>Oxford University Press</pub><pmid>18687674</pmid><doi>10.1093/dnares/dsn018</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext_linktorsrc |
| identifier | ISSN: 1340-2838 |
| ispartof | DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 2008-10, Vol.15 (5), p.285-295 |
| issn | 1340-2838 1756-1663 1875-6190 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2575888 |
| source | Access via Oxford University Press (Open Access Collection) |
| subjects | Base Sequence Biological and medical sciences Chromosome Mapping Chromosomes, Plant Databases, Nucleic Acid DNA, Complementary - genetics DNA, Plant - genetics Fundamental and applied biological sciences. Psychology Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Genome, Plant Molecular and cellular biology Molecular genetics Oryza - genetics Oryza rufipogon Oryza sativa |
| title | Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943 |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T22%3A47%3A31IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_TOX&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Collection%20and%20Comparative%20Analysis%20of%201888%20Full-length%20cDNAs%20from%20Wild%20Rice%20Oryza%20rufipogon%20Griff.%20W1943&rft.jtitle=DNA%20Research:%20An%20International%20Journal%20for%20Rapid%20Publication%20of%20Reports%20on%20Genes%20and%20Genomes&rft.au=Lu,%20Tingting&rft.date=2008-10-01&rft.volume=15&rft.issue=5&rft.spage=285&rft.epage=295&rft.pages=285-295&rft.issn=1340-2838&rft.eissn=1756-1663&rft_id=info:doi/10.1093/dnares/dsn018&rft_dat=%3Cproquest_TOX%3E20250828%3C/proquest_TOX%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=20250828&rft_id=info:pmid/18687674&rft_oup_id=10.1093/dnares/dsn018&rfr_iscdi=true |